Hello All,
I am currently trying to run low mode MD (LMOD) using Amber 12 using a
protocol I developed using Amber 10 and have run into the following error:
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Furthermore, the each cycle of LMOD minimization completes in three steps,
as opposed to the 40-70 steps that the same structure takes in Amber 10,
indicating that Amber 12 is doing something fundamentally different as I
tested my protocol in both Amber 10 and Amber 12 on the _exact_ same
structure. I have tried decreasing the number of steps to 50 and the
energy window to 0 and still get the same error.
Below is my lmod.in file, and any suggestions as to how to get LMOD to work
in Amber 12 would be greatly apperciated.
Thanks!
~Sarah
for lyA-p lyT 10-mer: initial minimization prior to MD
&cntrl
cut = 99.0,
ntx = 1,
irest = 0,
ipol = 0,
ntb = 0,
igb = 0,
imin = 1,
maxcyc = 5000,
ntmin = 4,
drms = 0.2,
ntpr = 1,
/
&lmod
conflib_size = 20,
number_lmod_iterations = 2,
total_low_modes = 10,
explored_low_modes = 3,
number_free_rotrans_modes = 6,
energy_window = 50.0,
lmod_minimize_grms = 0.1,
arnoldi_dimension = 0,
matrix_vector_product_method = 'forward',
frequency_eigenvector_recalc = 6,
lmod_restart_frequency = 6,
restart_pool_size = 3,
number_lmod_moves = 0,
lmod_step_size_max = 5.0,
lmod_step_size_min = 2.0,
lmod_relax_grms = 1.0,
Monte_Carlo_method = 'Metropolis',
rtemperature = 1.5,
number_ligands = 0,
conflib_filename = 'vancomycin_lmod_conflib',
lmod_trajectory_filename = 'vancomycin_lmod_trajectory',
lmod_job_title = 'vancomycin lmod test job',
lmod_verbosity = 2,
random_seed = 314159,
lbfgs_memory_depth = 3,
xmin_method = 'LBFGS',
xmin_verbosity = 0
/
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Received on Mon Nov 26 2012 - 11:30:02 PST
